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THEMIS Conventions for Death Table to Allow Multiple Records - Version 5.4

CDM Builders
#1

This is an open forum discussion for:
THEMIS issue #79
Multiple Death Records Due to Death_type or Cause - Version 5.4

This issue has been discussed multiple times over multiple years (see Related Posts below). There has even been a THEMIS thread proposing a solution. However, the issue remains, and we’d like to stick a pin in it for good.

Issue Name: Multiple Death Records Due to Death_type_concept or Cause_concept Version 5.4

Issue Type: Duplicate records caused by multiple standard concept_ids for death cause or death type (provenance)

Description: OMOP CDM v5.4
The table description for the Death table has the following: “A person can have up to one record if the source system contains evidence about the Death”. However, an ICD diagnosis code may map to multiple SNOMED codes:

ICD10: J96.21 (Acute on chronic respiratory failure with hypoxia (HCC))
maps to
SNOMED: 389086002 (Hypoxia) and 67905004 (Acute-on-chronic respiratory failure)
This results in two records with the same death date.

Similarly, a person may have death records from multiple systems (provenance), i.e. EHR and death registry.

Suggested Solution: For OMOP version 5.4, allow multiple records in the Death table caused by either the death_type_concept_id and/or cause_concept_id. However the Death_Date(s) must match.

Possible Implications:

  • CDM documentation will need to be modified.
  • The rules of the DQD (Data Quality Dashboard) will have to be adjusted to match. @clairblacketer
  • Question @Chris_Knoll on whether this change will affect Atlas. Does Atlas expect only one death record?

Related forum posts:

Reported By: Roger Carlson
@Chris_Knoll @Christian_Reich @katy-sadowski @MPhilofsky @clairblacketer @lychenus13 @Polina_Talapova @ericaVoss @QI_omop @Mark @hiro-mishima @cukarthik @PriyaDesai @jmethot @Vojtech_Huser @aostropolets @pavgra @Patrick_Ryan

2 Likes
Should death reason be also in the condition_occurrence table in cdm5.3/5.4?
Multiple Death records due to SNOMED mapping
Multiple Cause of Death
Condition_occurrence, Death diagnoses
Multiple death records from different sources
#2

There has been no discussion on this. I’m bumping it. :slightly_smiling_face:

#3

I have another potential solution that may not impact tooling as much.

Preferred Concepts Based on Context (Death)

Process

  • ETL creates multiple records, then drops duplicates keeping the single ‘preferred’ concept_id for the context.
  • Both records must have the same person_id, date, and death_type_id for this drop to occur
  • All dropped records with non-preferred concept-id’s would be retained in cause_source_value as a list VARCHAR[code1, code2, code3]

Example:
In the context of cause of death, ICD10(J96.21) maps to SNOMED(67905004 (Acute-on-chronic respiratory failure)) would be the preferred term and used as the cause_id.

Both codes would be included in cause_source_value as a list [67905004, 389086002] with the preferred term being first.

Rationale:

  1. Hypoxia is a disposition (an intrinsic characteristic) of the object(person) in the state of reduced oxygen supply to tissue.
    - This state can be both chronic (e.g., COPD) and emergent (e.g., asphyxiation).
    - This state can be the result of singular or plural system deterioration and is an inherent feature of the object(person) respiratory or circulatory system.

  2. Acute-on-chronic respiratory failure is both a disposition and a role (context dependent) of the object(person) in the state of critically deteriorated respiratory function
    - This state is temporary (it will either be recovered from or be fatal).
    - This state is not an inherent feature of the respiratory system, it is contingent on the current state of the object(person) health.

  3. Acute-on-chronic respiratory failure would be the ‘preferred’ concept_id as a cause of death because it more accurately aligns with a direct cause of death.

Pros:

  • Increase accuracy for cause of death.
  • Tooling would not need to be adjusted or re-coded.

Cons:

  • Potentially significant undertaking by the Vocabulary WG to create ‘preferred’ concept lists for cause of death for each vocabulary.
  • We would need to find a feasible way to distribute the ‘preferred’ concept list. This could through using one of the concept tables or establishing a ‘Death’ domain.
  • VARCHAR is a bad way to save lists and not all programming languages and database systems interpret lists the same way (this more of a technical issue for reproducibility or reversing an ETL)
#4

Now that the Holidays are over, I’m getting back to this.

My original solution was ETL-centric, since I’m an ETL guy. I don’t have any idea of the ‘re-tooling’ that will be needed as a result if it. Does anyone know specifically what re-tooling will be required? To which products?

Hayden’s solution requires a heavier ETL modification, which I suppose is to be preferred overall. But I’m not sure who would be responsible to create preferred concept_ids or how to go about doing it.

Overall, I think the original proposal is less complicated.

This is not a new issue. Everyone who has cause_of_death in the death table has had to deal with in in some way.

What are others doing?

@Chris_Knoll @Christian_Reich @katy-sadowski @MPhilofsky @clairblacketer @lychenus13 @Polina_Talapova @ericaVoss @QI_omop @Mark @hiro-mishima @cukarthik @PriyaDesai @jmethot @Vojtech_Huser @aostropolets @pavgra @Patrick_Ryan

#5

This is another case where forcing document type data into a relational data format causes issues. What ever the solution is chosen, no data should be dropped, no matter how painful it is to us ETL’er; I do not like the idea of dropping any concepts.

As outpatient only, we rarely have the cause of death, almost all of ours will be ‘0’. Perhaps I am not the best one to be commenting on this topic :expressionless: but I hate the idea of lost data.

#6

While Hayden’s solution is interesting and accurate from a physiological point of view, it doesn’t solve for the case when a site has more than one source for death data.

@Chris_Knoll, as the OHDSI forums Atlas guru, will having > 1 death record for a person break or cause unnecessary harm to an Atlas study? The death records for a person would all have the same date. Only the cause_concept_id and death_type_concept_id would be allowed to be different between death records for a person.

#7

Not that I can think of…the way it works is Death criteria just looks at the Death table, I don’t think there would be an issue if there were multiple records in there.

#8

Thanks for the speedy reply, @Chris_Knoll!

#9

This issue has been out here for some time without any objections. Here is one last call for any objection before we put it on the Themis agenda for ratification.

@katy-sadowski Do we have a one death record per person check?

#10

@MPhilofsky we do not!

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